pathWAS_MRInput: Create MR Input object for MVMR

In Sabor117/PathWAS: Creates predictive models of biological pathway functionality

Create MR Input object for MVMR

Description

Inputs and combines aspects from your QTL SNPs, clumped SNPs, pathway genes, and omics summary stats (plus flip status) and creates MR input object.

Usage

pathWAS_MRInput(
  genelist,
  clumped_snps,
  qtl_sumstats,
  geneCol = "gene",
  omics_snps,
  omics_SNPCol = "rsid",
  omics_BetaCol = "beta1",
  omics_SECol = "se",
  end_point = "endprotein",
  verbose = TRUE
)

Arguments

genelist	list. List of genes extracted from database for your pathway which overlap with your QTL data.
clumped_snps	data frame. The data frame of clumped SNPs output from qtl_clumpR.
qtl_sumstats	character. File location for the QTLs used (either divided by gene or complete data).
geneCol	character. Name or number of column containing the name of the gene for each SNP in the QTL data. Default is "gene". Ensure the format of the name is the same as your gene list.
omics_snps	data frame. Summary stats of end-point omcis, now including FLIP column frm omics_MungeR
omics_SNPCol	character. Name/number of column containing the SNP ID in the omics data frame.
omics_BetaCol	character. Name/number of column containing the effect size in the omics data frame.
omics_SECol	character. Name/number of column containing the standard error in the omics data frame.

Details

This is a shortened version of the pathWAS_MR() function designed to solely output the same MR input object used in the mr_mvinput() function if PathWAS. Created primarily for use with the pathWAS_snpCheck function in mind.

Examples

## Having created a list of genes, clumped SNPs and munged your Omics SNPs you can input them in the following way, along with adding the option to save the MR output:
pathWAS_MR(genelist, clumped_snps, qtl_sumstats = "/opt/localdir/gene_qtls/file1_sumstats_$$$.tsv", geneCol = "gene_ensembl", omics_snps, save_MROutput = TRUE, save_MROutLoc = "/opt/localdir/mr_outputs/", path_select = "nod_signalling", end_point = "IL18")

Sabor117/PathWAS documentation built on Nov. 29, 2024, 7:44 a.m.